Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose
Abstract
Background: Biofuel production from plant cell walls offers the potential for sustainable and economically attractive alternatives to petroleum-based products. In particular, Clostridium thermocellum is a promising host for consolidated bioprocessing (CBP) because of its strong native ability to ferment cellulose. Results: We tested 12 different enzyme combinations to identify an n-butanol pathway with high titer and thermostability in C. thermocellum. The best producing strain contained the thiolase–hydroxybutyryl-CoA dehydrogenase– crotonase (Thl-Hbd-Crt) module from Thermoanaerobacter thermosaccharolyticum, the trans-enoyl-CoA reductase (Ter) enzyme from Spirochaeta thermophila and the butyraldehyde dehydrogenase and alcohol dehydrogenase (BadBdh) module from Thermoanaerobacter sp. X514 and was able to produce 88 mg/L n-butanol. The key enzymes from this combination were further optimized by protein engineering. The Thl enzyme was engineered by introducing homologous mutations previously identified in Clostridium acetobutylicum. The Hbd and Ter enzymes were engineered for changes in cofactor specificity using the CSR-SALAD algorithm to guide the selection of mutations. The cofactor engineering of Hbd had the unexpected side effect of also increasing activity by 50-fold. Conclusions: Here we report engineering C. thermocellum to produce n-butanol. Our initial pathway designs resulted in low levels (88 mg/L) of n-butanol production. By engineering the protein sequence of key enzymes in themore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER), Center for Bioenergy Innovation; DOE Joint Genome Institute
- OSTI Identifier:
- 1618768
- Alternate Identifier(s):
- OSTI ID: 1627002
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Name: Biotechnology for Biofuels Journal Volume: 12 Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Energy & Fuels; Cellulosic biofuel; Clostridium thermocellum; Consolidated bioprocessing; n-Butanol; Protein engineering
Citation Formats
Tian, Liang, Conway, Peter M., Cervenka, Nicholas D., Cui, Jingxuan, Maloney, Marybeth, Olson, Daniel G., and Lynd, Lee R. Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose. Netherlands: N. p., 2019.
Web. doi:10.1186/s13068-019-1524-6.
Tian, Liang, Conway, Peter M., Cervenka, Nicholas D., Cui, Jingxuan, Maloney, Marybeth, Olson, Daniel G., & Lynd, Lee R. Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose. Netherlands. https://doi.org/10.1186/s13068-019-1524-6
Tian, Liang, Conway, Peter M., Cervenka, Nicholas D., Cui, Jingxuan, Maloney, Marybeth, Olson, Daniel G., and Lynd, Lee R. Tue .
"Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose". Netherlands. https://doi.org/10.1186/s13068-019-1524-6.
@article{osti_1618768,
title = {Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose},
author = {Tian, Liang and Conway, Peter M. and Cervenka, Nicholas D. and Cui, Jingxuan and Maloney, Marybeth and Olson, Daniel G. and Lynd, Lee R.},
abstractNote = {Background: Biofuel production from plant cell walls offers the potential for sustainable and economically attractive alternatives to petroleum-based products. In particular, Clostridium thermocellum is a promising host for consolidated bioprocessing (CBP) because of its strong native ability to ferment cellulose. Results: We tested 12 different enzyme combinations to identify an n-butanol pathway with high titer and thermostability in C. thermocellum. The best producing strain contained the thiolase–hydroxybutyryl-CoA dehydrogenase– crotonase (Thl-Hbd-Crt) module from Thermoanaerobacter thermosaccharolyticum, the trans-enoyl-CoA reductase (Ter) enzyme from Spirochaeta thermophila and the butyraldehyde dehydrogenase and alcohol dehydrogenase (BadBdh) module from Thermoanaerobacter sp. X514 and was able to produce 88 mg/L n-butanol. The key enzymes from this combination were further optimized by protein engineering. The Thl enzyme was engineered by introducing homologous mutations previously identified in Clostridium acetobutylicum. The Hbd and Ter enzymes were engineered for changes in cofactor specificity using the CSR-SALAD algorithm to guide the selection of mutations. The cofactor engineering of Hbd had the unexpected side effect of also increasing activity by 50-fold. Conclusions: Here we report engineering C. thermocellum to produce n-butanol. Our initial pathway designs resulted in low levels (88 mg/L) of n-butanol production. By engineering the protein sequence of key enzymes in the pathway, we increased the n-butanol titer by 2.2-fold. We further increased n-butanol production by adding ethanol to the growth media. By combining all these improvements, the engineered strain was able to produce 357 mg/L of n-butanol from cellulose within 120 h.},
doi = {10.1186/s13068-019-1524-6},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 12,
place = {Netherlands},
year = {Tue Jul 23 00:00:00 EDT 2019},
month = {Tue Jul 23 00:00:00 EDT 2019}
}
https://doi.org/10.1186/s13068-019-1524-6
Web of Science
Figures / Tables:
Works referenced in this record:
A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum
journal, November 2015
- Yoo, Minyeong; Bestel-Corre, Gwenaelle; Croux, Christian
- mBio, Vol. 6, Issue 6
Transformation of Clostridium Thermocellum by Electroporation
book, January 2012
- Olson, Daniel G.; Lynd, Lee R.
- Cellulases
Unique genetic cassettes in a Thermoanaerobacterium contribute to simultaneous conversion of cellulose and monosugars into butanol
journal, March 2018
- Li, Tinggang; Zhang, Chen; Yang, Kun-Lin
- Science Advances, Vol. 4, Issue 3
Glycolysis without pyruvate kinase in Clostridium thermocellum
journal, January 2017
- Olson, Daniel G.; Hörl, Manuel; Fuhrer, Tobias
- Metabolic Engineering, Vol. 39
Biochemical and Structural Characterization of the trans -Enoyl-CoA Reductase from Treponema denticola
journal, August 2012
- Bond-Watts, Brooks B.; Weeks, Amy M.; Chang, Michelle C. Y.
- Biochemistry, Vol. 51, Issue 34
Fermentative production of butanol—the industrial perspective
journal, June 2011
- Green, Edward M.
- Current Opinion in Biotechnology, Vol. 22, Issue 3
Reviving the Weizmann process for commercial n-butanol production
journal, September 2018
- Nguyen, Ngoc-Phuong-Thao; Raynaud, Céline; Meynial-Salles, Isabelle
- Nature Communications, Vol. 9, Issue 1
A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol
journal, February 2019
- Tian, Liang; Cervenka, Nicholas D.; Low, Aidan M.
- Scientific Reports, Vol. 9, Issue 1
Thiolase engineering for enhanced butanol production in Clostridium acetobutylicum
journal, November 2012
- Mann, Miriam S.; Lütke-Eversloh, Tina
- Biotechnology and Bioengineering, Vol. 110, Issue 3
Metabolic and process engineering of Clostridium cellulovorans for biofuel production from cellulose
journal, November 2015
- Yang, Xiaorui; Xu, Mengmeng; Yang, Shang-Tian
- Metabolic Engineering, Vol. 32
Bacterial genomes: what they teach us about cellulose degradation
journal, November 2013
- Brumm, Phillip J.
- Biofuels, Vol. 4, Issue 6
Consolidated bioprocessing of cellulosic biomass: an update
journal, October 2005
- Lynd, Lee R.; van Zyl, Willem H.; McBride, John E.
- Current Opinion in Biotechnology, Vol. 16, Issue 5, p. 577-583
Thermoanaerobacter species differ in their potential to reduce organic acids to their corresponding alcohols
journal, July 2018
- Hitschler, Lisa; Kuntz, Michelle; Langschied, Felix
- Applied Microbiology and Biotechnology, Vol. 102, Issue 19
Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure
journal, November 2017
- Brunecky, Roman; Alahuhta, Markus; Sammond, Deanne W.
- Biotechnology for Biofuels, Vol. 10, Issue 1
ATP drives direct photosynthetic production of 1-butanol in cyanobacteria
journal, April 2012
- Lan, E. I.; Liao, J. C.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways
journal, February 2011
- Bond-Watts, Brooks B.; Bellerose, Robert J.; Chang, Michelle C. Y.
- Nature Chemical Biology, Vol. 7, Issue 4
Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains
journal, July 2014
- Lian, Jiazhang; Si, Tong; Nair, Nikhil U.
- Metabolic Engineering, Vol. 24
A hybrid synthetic pathway for butanol production by a hyperthermophilic microbe
journal, January 2015
- Keller, Matthew W.; Lipscomb, Gina L.; Loder, Andrew J.
- Metabolic Engineering, Vol. 27
Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485
journal, September 2015
- Zhou, Jilai; Olson, Daniel G.; Lanahan, Anthony A.
- Biotechnology for Biofuels, Vol. 8, Issue 1
Novel high-efficient butanol production from butyrate by non-growing Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) with methyl viologen
journal, September 2007
- Tashiro, Yukihiro; Shinto, Hideaki; Hayashi, Miki
- Journal of Bioscience and Bioengineering, Vol. 104, Issue 3
Recent progress in consolidated bioprocessing
journal, June 2012
- Olson, Daniel G.; McBride, John E.; Joe Shaw, A.
- Current Opinion in Biotechnology, Vol. 23, Issue 3, p. 396-405
The grand challenge of cellulosic biofuels
journal, October 2017
- Lynd, Lee R.
- Nature Biotechnology, Vol. 35, Issue 10
Engineering electron metabolism to increase ethanol production in Clostridium thermocellum
journal, January 2017
- Lo, Jonathan; Olson, Daniel G.; Murphy, Sean Jean-Loup
- Metabolic Engineering, Vol. 39
Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae
journal, May 2016
- Shi, Shuobo; Si, Tong; Liu, Zihe
- Scientific Reports, Vol. 6, Issue 1
Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose
journal, January 2016
- Gaida, Stefan Marcus; Liedtke, Andrea; Jentges, Andreas Heinz Wilhelm
- Microbial Cell Factories, Vol. 15, Issue 1
Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature
journal, December 2016
- Groom, Joseph; Chung, Daehwan; Olson, Daniel G.
- Metabolic Engineering Communications, Vol. 3
Increase in Ethanol Yield via Elimination of Lactate Production in an Ethanol-Tolerant Mutant of Clostridium thermocellum
journal, February 2014
- Biswas, Ranjita; Prabhu, Sandeep; Lynd, Lee R.
- PLoS ONE, Vol. 9, Issue 2
Elucidation of the roles of adhE1 and adhE2 in the primary metabolism of Clostridium acetobutylicum by combining in-frame gene deletion and a quantitative system-scale approach
journal, April 2016
- Yoo, Minyeong; Croux, Christian; Meynial-Salles, Isabelle
- Biotechnology for Biofuels, Vol. 9, Issue 1
Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum
journal, June 2016
- Tian, Liang; Papanek, Beth; Olson, Daniel G.
- Biotechnology for Biofuels, Vol. 9, Issue 1
Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production
journal, September 2018
- Hon, Shuen; Holwerda, Evert K.; Worthen, Robert S.
- Biotechnology for Biofuels, Vol. 11, Issue 1
Ferredoxin:NAD + Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation
journal, September 2016
- Tian, Liang; Lo, Jonathan; Shao, Xiongjun
- Applied and Environmental Microbiology, Vol. 82, Issue 24
eQuilibrator--the biochemical thermodynamics calculator
journal, November 2011
- Flamholz, A.; Noor, E.; Bar-Even, A.
- Nucleic Acids Research, Vol. 40, Issue D1
A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases
journal, October 2016
- Cahn, Jackson K. B.; Werlang, Caroline A.; Baumschlager, Armin
- ACS Synthetic Biology, Vol. 6, Issue 2
Enhanced ethanol formation by Clostridium thermocellum via pyruvate decarboxylase
journal, October 2017
- Tian, Liang; Perot, Skyler J.; Hon, Shuen
- Microbial Cell Factories, Vol. 16, Issue 1
Microbial n -butanol production from Clostridia to non-Clostridial hosts
journal, October 2013
- Branduardi, Paola; de Ferra, Francesca; Longo, Valeria
- Engineering in Life Sciences, Vol. 14, Issue 1
The Bifunctional Alcohol and Aldehyde Dehydrogenase Gene, adhE , Is Necessary for Ethanol Production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum
journal, February 2015
- Lo, Jonathan; Zheng, Tianyong; Hon, Shuen
- Journal of Bacteriology, Vol. 197, Issue 8
Automated design of synthetic ribosome binding sites to control protein expression
journal, October 2009
- Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A.
- Nature Biotechnology, Vol. 27, Issue 10, p. 946-950
Identifying promoters for gene expression in Clostridium thermocellum
journal, December 2015
- Olson, Daniel G.; Maloney, Marybeth; Lanahan, Anthony A.
- Metabolic Engineering Communications, Vol. 2
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
journal, April 2014
- Chin, Ju Xin; Chung, Bevan Kai-Sheng; Lee, Dong-Yup
- Bioinformatics, Vol. 30, Issue 15
Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum
journal, September 2015
- Kim, Sangwoo; Jang, Yu-Sin; Ha, Sung-Chul
- Nature Communications, Vol. 6, Issue 1
Enzymatic Assembly of Overlapping DNA Fragments
book, May 2011
- Gibson, Daniel G.
- Methods in Enzymology
Reducing GHG emissions in the United States' transportation sector
journal, June 2011
- Andress, David; Nguyen, T. Dean; Das, Sujit
- Energy for Sustainable Development, Vol. 15, Issue 2
Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen
journal, December 2014
- Dai, Xin; Tian, Yan; Li, Jinting
- Applied and Environmental Microbiology, Vol. 81, Issue 4
The ethanol pathway from Thermoanaerobacterium saccharolyticum improves ethanol production in Clostridium thermocellum
journal, July 2017
- Hon, Shuen; Olson, Daniel G.; Holwerda, Evert K.
- Metabolic Engineering, Vol. 42
Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum
journal, September 2015
- Lin, Paul P.; Mi, Luo; Morioka, Amy H.
- Metabolic Engineering, Vol. 31
Lignocellulose fermentation and residual solids characterization for senescent switchgrass fermentation by Clostridium thermocellum in the presence and absence of continuous in situ ball-milling
journal, January 2017
- Balch, Michael L.; Holwerda, Evert K.; Davis, Mark F.
- Energy & Environmental Science, Vol. 10, Issue 5
Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production
journal, January 2014
- Bhandiwad, Ashwini; Shaw, A. Joe; Guss, Adam
- Metabolic Engineering, Vol. 21
Fermentative butanol production by clostridia
journal, October 2008
- Lee, Sang Yup; Park, Jin Hwan; Jang, Seh Hee
- Biotechnology and Bioengineering, Vol. 101, Issue 2, p. 209-228